OperaMate: An R package of Data Importing, Processing and Analysis for Opera High Content Screening System
Version 1.8.0

OperaMate is a flexible R package dealing with the data generated by PerkinElmer's Opera High Content Screening System. The functions include the data importing, normalization and quality control, hit detection and function analysis.

AuthorChenglin Liu
Bioconductor views CellBasedAssays Normalization Preprocessing QualityControl
Date of publicationNone
MaintainerChenglin Liu <cliu@sjtu.edu.cn>
LicenseGPL (>= 3)
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("OperaMate")

Popular man pages

cellData-class: The cellData class
cellNorm: Data normalization
cellNumLoad: Load cell number
cellSig: Hit identification
cellSigAnalysis: Hits function analysis
data: Examples of tables and cellData objects
expData-class: The expData class
See all...

All man pages Function index File listing

Man pages

cellData-class: The cellData class
cellLoad: Data importing
cellMean: Mean of two cellData objects
cellNorm: Data normalization
cellNumLoad: Load cell number
cellQC: Quality control
cellSig: Hit identification
cellSigAnalysis: Hits function analysis
cellSigAnalysisPlot: The barplot of enrichment functions
cellSigPlot: Hits volcano plot
cellViz: Data visualization
data: Examples of tables and cellData objects
expData-class: The expData class
generateReport: Report generation
loadAll: Data importing
nameParser: Plate information extraction
operaMate: Data process and analysis pipeline
parseTemplete: Data extraction from one report

Functions

[, Man page
[,cellData,character,ANY-method Man page
[,expData,ANY,ANY-method Man page
addNatoSudoRep Source code
cellBoxplot Source code
cellData Man page Source code
cellData, Man page
cellData-class Man page
cellData-method Man page
cellHeatmap Source code
cellLoad Man page
cellLoad,cellData-method Man page
cellMean Man page
cellMean,cellData,cellData,character-method Man page
cellNorm Man page
cellNorm,cellData-method Man page
cellNumLoad Man page
cellNumLoad,cellData,cellData-method Man page
cellNumberReshape Source code
cellQC Man page
cellQC,cellData-method Man page
cellSig Man page
cellSig,cellData-method Man page
cellSigAnalysis Man page Source code
cellSigAnalysisPlot Man page Source code
cellSigPlot Man page Source code
cellViz Man page Source code
dataLoad Man page
dataLoad, Man page
dataLoad,expData-method Man page
demoData Man page
expData Man page Source code
expData, Man page
expData-class Man page
expData-method Man page
fitStable Source code
gDevice.new Source code
generateReport Man page Source code
loadAll Man page Source code
nameParser Man page Source code
onCellNum Man page
onLoad Source code
onUnload Source code
oneCell Man page
oneCellNum Man page
operaMate Man page Source code
parseFullTab Source code
parseMatrix Source code
parseTab Source code
parseTemplete Man page Source code
plateCorrelationPlot Source code
plateCorrelationTest Source code
plateQC Source code
platemap Man page
show,cellData-method Man page
show,expData-method Man page
showPlate Source code
sigByTTest Source code
sigDetect Source code
wellQC Source code
zFactorTest Source code

Files

DESCRIPTION
NAMESPACE
R
R/cellData-class.R
R/cellData-methods.R
R/dataprocess.R
R/expData-class.R
R/expData-methods.R
R/functions.R
R/zzz.R
build
build/vignette.rds
data
data/demoCell.rda
data/demoCellNum.rda
data/platemap.rda
inst
inst/Test
inst/Test/Matrix
inst/Test/Matrix/130504-s1-02.txt
inst/Test/Matrix/130504-s1-03.txt
inst/Test/Matrix/Matrix.130506-s2-02.txt
inst/Test/Matrix/Matrix.130506-s2-03.txt
inst/Test/Matrix/Matrix.130508-s3-02.txt
inst/Test/Matrix/Matrix.130508-s3-03.txt
inst/Test/Matrix/Matrix.130607-s1-04.txt
inst/Test/Matrix/Matrix.130609-s2-04.txt
inst/Test/Matrix/Matrix.130611-s3-04.txt
inst/Test/Tab
inst/Test/Tab/Tab.130504-s1-01.txt
inst/Test/Tab/Tab.130506-s2-01.txt
inst/Test/Tab/Tab.130508-s3-01.txt
inst/Test/demoData
inst/Test/demoData/demoParam.txt
inst/Test/demoData/genemap.csv
inst/doc
inst/doc/OperaMate-manual.pdf
inst/doc/OperaMate-vignette.R
inst/doc/OperaMate-vignette.Rnw
inst/doc/OperaMate-vignette.pdf
inst/doc/param.txt
man
man/cellData-class.Rd
man/cellLoad.Rd
man/cellMean.Rd
man/cellNorm.Rd
man/cellNumLoad.Rd
man/cellQC.Rd
man/cellSig.Rd
man/cellSigAnalysis.Rd
man/cellSigAnalysisPlot.Rd
man/cellSigPlot.Rd
man/cellViz.Rd
man/data.Rd
man/expData-class.Rd
man/generateReport.Rd
man/loadAll.Rd
man/nameParser.Rd
man/operaMate.Rd
man/parseTemplete.Rd
vignettes
vignettes/OperaMate-vignette.Rnw
vignettes/OperaMate-vignette.bib
vignettes/normplot.png
vignettes/qcplot.png
vignettes/sigplot.png
OperaMate documentation built on May 20, 2017, 10:52 p.m.

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